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- PDB-5nvk: Crystal structure of the human 4EHP-GIGYF1 complex -

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Basic information

Entry
Database: PDB / ID: 5nvk
TitleCrystal structure of the human 4EHP-GIGYF1 complex
Components
  • Eukaryotic translation initiation factor 4E type 2
  • GRB10-interacting GYF protein 1
KeywordsTRANSLATION / translational regulation / cap-binding protein / 4EHP-binding protein / GRB10-interacting GYF protein 1
Function / homology
Function and homology information


RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / negative regulation of translational initiation / translation initiation factor activity / rescue of stalled ribosome ...RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / negative regulation of translational initiation / translation initiation factor activity / rescue of stalled ribosome / insulin-like growth factor receptor signaling pathway / translational initiation / P-body / ISG15 antiviral mechanism / negative regulation of translation / ubiquitin protein ligase binding / protein-containing complex / RNA binding / cytosol / cytoplasm
Similarity search - Function
GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e ...GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E type 2 / GRB10-interacting GYF protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPeter, D. / Valkov, E.
CitationJournal: Genes Dev. / Year: 2017
Title: GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression.
Authors: Peter, D. / Weber, R. / Sandmeir, F. / Wohlbold, L. / Helms, S. / Bawankar, P. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E type 2
B: GRB10-interacting GYF protein 1
C: Eukaryotic translation initiation factor 4E type 2
D: GRB10-interacting GYF protein 1
E: Eukaryotic translation initiation factor 4E type 2
F: GRB10-interacting GYF protein 1
G: Eukaryotic translation initiation factor 4E type 2
H: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)122,8488
Polymers122,8488
Non-polymers00
Water00
1
A: Eukaryotic translation initiation factor 4E type 2
B: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area13030 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E type 2
D: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-23 kcal/mol
Surface area13810 Å2
MethodPISA
3
E: Eukaryotic translation initiation factor 4E type 2
F: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-26 kcal/mol
Surface area12530 Å2
MethodPISA
4
G: Eukaryotic translation initiation factor 4E type 2
H: GRB10-interacting GYF protein 1


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.320, 135.320, 60.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
Eukaryotic translation initiation factor 4E type 2 / eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic ...eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic translation initiation factor 4E-like 3 / eIF4E-like protein 4E-LP / mRNA cap-binding protein 4EHP / h4EHP / mRNA cap-binding protein type 3


Mass: 21979.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: the first residue of the coordinate sequence of chain G belongs to the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E2, EIF4EL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O60573
#2: Protein
GRB10-interacting GYF protein 1 / PERQ amino acid-rich with GYF domain-containing protein 1


Mass: 8732.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIGYF1, CDS2, PERQ1, PP3360 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O75420

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 0.2 M KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99981 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99981 Å / Relative weight: 1
ReflectionResolution: 2.9→47.843 Å / Num. obs: 24699 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rsym value: 0.111 / Net I/σ(I): 10.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.95 / Num. unique all: 1782 / Rsym value: 0.647 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NVL

5nvl


Resolution: 2.9→47.843 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1218 4.93 %Random selection
Rwork0.2042 ---
obs0.2067 24694 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7833 0 0 0 7833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038014
X-RAY DIFFRACTIONf_angle_d0.49410834
X-RAY DIFFRACTIONf_dihedral_angle_d16.4554839
X-RAY DIFFRACTIONf_chiral_restr0.0391152
X-RAY DIFFRACTIONf_plane_restr0.0031404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.01620.32061300.28872564X-RAY DIFFRACTION100
3.0162-3.15350.35211280.25982628X-RAY DIFFRACTION100
3.1535-3.31970.32821420.25782555X-RAY DIFFRACTION100
3.3197-3.52760.28861470.2382582X-RAY DIFFRACTION100
3.5276-3.79990.27121390.21522607X-RAY DIFFRACTION100
3.7999-4.18210.24521390.1962572X-RAY DIFFRACTION100
4.1821-4.78680.20281320.16732625X-RAY DIFFRACTION99
4.7868-6.02890.21541380.1752621X-RAY DIFFRACTION100
6.0289-47.84930.2231230.17892722X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2925-0.0402-0.0741.5824-0.06650.38050.03660.09950.0666-0.1059-0.01330.19340.0238-0.11340.00260.4310.026-0.01540.46770.0190.1218-10.992316.3599-38.3102
22.1754-0.8313-0.18351.801-0.33121.5434-0.1559-0.13380.08620.28260.11660.1999-0.0965-0.27110.02790.5145-0.04630.04510.3997-0.01860.1786-14.053424.4844-28.238
32.99980.0895-0.54352.33130.43292.98290.1877-0.06070.4891-0.04370.0364-0.3584-0.51570.13-0.14680.45490.00340.08810.3089-0.04580.31645.841748.6068-28.1842
42.7799-0.04210.50391.46460.6771.57070.21150.04980.25580.24860.0391-0.4911-0.0930.115-0.30350.5794-0.04910.01630.4683-0.00170.31717.761338.7647-35.1999
51.4576-0.112-0.1192.28940.03831.5892-0.144-0.35860.05840.48190.18590.3288-0.1073-0.30060.09970.51690.09620.03860.6521-0.08260.191619.42976.7465-1.2315
61.0252-0.13480.46730.40510.27680.9839-0.255-0.27160.33050.61890.0819-0.1172-0.22840.273-0.10170.66780.0605-0.07590.5816-0.10330.265630.375481.668-6.0963
72.7707-0.06250.29480.2239-0.04751.1649-0.10670.1509-0.2906-0.05650.1239-0.01920.15230.05260.00050.4384-0.00430.01850.3824-0.06640.182650.509357.9738-10.0165
82.2787-0.44140.22550.4524-0.05191.50260.0174-0.4758-0.50280.0976-0.05890.1580.2921-0.04290.06250.5198-0.03530.04620.52430.05140.232842.254955.25380.2461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 52 through 232)
2X-RAY DIFFRACTION2(chain 'B' and resid 36 through 103)
3X-RAY DIFFRACTION3(chain 'C' and resid 52 through 219)
4X-RAY DIFFRACTION4(chain 'D' and resid 30 through 103)
5X-RAY DIFFRACTION5(chain 'E' and resid 52 through 219)
6X-RAY DIFFRACTION6(chain 'F' and resid 37 through 103)
7X-RAY DIFFRACTION7(chain 'G' and resid 51 through 233)
8X-RAY DIFFRACTION8(chain 'H' and resid 38 through 103)

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